PDB-8y2l: The Crystal Structure of Glucosyltransferase TcdB from Clostridio...

ID or keywords:

Entry

Database: PDB / ID: 8y2l

Title

The Crystal Structure of Glucosyltransferase TcdB from Clostridioides difficile

Components

Glucosyltransferase TcdB

Keywords

TRANSFERASE / Glucosyltransferase

Function / homology

Function and homology information

glucosyltransferase activity / host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / cysteine-type peptidase activity / host cell endosome membrane / toxin activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lipid binding / host cell plasma membrane / proteolysis ...
Similarity search - Function

Biological species

Clostridioides difficile (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.95 Å

Authors

Fan, S. / Wei, X. / Lv, R. / Wang, C. / Tang, M. / Jin, Y. / Yang, Z.

Funding support

1items

Citation

Journal: To Be Published
Title: The Crystal Structure of Glucosyltransferase TcdB from Clostridioides difficile
Authors: Fan, S. / Wei, X. / Lv, R. / Wang, C. / Tang, M. / Jin, Y. / Yang, Z.

History

Deposition	Jan 26, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jan 29, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8y2l.cif.gz	346.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8y2l.ent.gz	274.1 KB	Display	PDB format
PDBx/mmJSON format	8y2l.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y2/8y2l ftp://data.pdbj.org/pub/pdb/validation_reports/y2/8y2l	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#138 - Jun 2011 Glucansucrase similarity (4) #156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (2) #254 - Feb 2021 Cellulose Synthase similarity (2) #141 - Sep 2011 O-GlcNAc Transferase similarity (1)

Deposited unit

A: Glucosyltransferase TcdB

B: Glucosyltransferase TcdB

C: Glucosyltransferase TcdB

hetero molecules

191 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	155.166, 268.755, 194.862
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A
3	2	A
4	2	A
5	3	A
6	3	A

NCS domain segments:

Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: PHE / End label comp-ID: PHE / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: -2 - 539 / Label seq-ID: 1 - 542

Dom-ID	Component-ID	Ens-ID
1	1	1
2	1	1
3	2	2
4	2	2
5	3	3
6	3	3

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6

#1: Protein	Glucosyltransferase TcdB Mass: 63164.566 Da / Num. of mol.: 3 / Mutation: Y59C, E244G, S452A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: tcdB, toxB / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P18177, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-UDP / URIDINE-5'-DIPHOSPHATE Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₉H₁₄N₂O₁₂P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 5.36 Å³/Da / Density % sol: 77.05 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.01M RbCl, 0.01M SrAc2, 0.01M CsAc, 0.01M BaAc2, 0.1M BES, TEA pH7.5, 12.5% PEG4,000, 20% 1,2,6- Hexanetriol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9537 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 16, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9537 Å / Relative weight: 1
Reflection	Resolution: 3.95→49.15 Å / Num. obs: 36051 / % possible obs: 99.9 % / Redundancy: 8.9 % / CC_1/2: 0.998 / Net I/σ(I): 10.2
Reflection shell	Resolution: 3.95→4.13 Å / Num. unique obs: 4300 / CC_1/2: 0.743

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0419	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.95→49.15 Å / Cor.coef. F_o:F_c: 0.914 / Cor.coef. F_o:F_c free: 0.887 / SU B: 40.116 / SU ML: 0.525 / Cross valid method: FREE R-VALUE / ESU R Free: 0.753
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.3002	1789	4.966 %
R_work	0.244	34235	-
all	0.247	-	-
obs	-	36024	99.917 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 147.016 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.927 Å²	-0 Å²	0 Å²
2-	-	-0.656 Å²	-0 Å²
3-	-	-	-2.271 Å²

Refinement step

Cycle: LAST / Resolution: 3.95→49.15 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13251	0	78	14	13343

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.002	0.012	13587
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	12630
X-RAY DIFFRACTION	r_angle_refined_deg	0.801	1.83	18321
X-RAY DIFFRACTION	r_angle_other_deg	0.319	1.775	29148
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.76	5	1623
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	3.079	5	54
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.762	10	2505
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	9.106	10	720
X-RAY DIFFRACTION	r_chiral_restr	0.039	0.2	2001
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.02	15870
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3144
X-RAY DIFFRACTION	r_nbd_refined	0.2	0.2	3162
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.17	0.2	12364
X-RAY DIFFRACTION	r_nbtor_refined	0.178	0.2	6821
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.069	0.2	6928
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.13	0.2	299
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.05	0.2	16
X-RAY DIFFRACTION	r_nbd_other	0.062	0.2	43
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.076	0.2	8
X-RAY DIFFRACTION	r_mcbond_it	4.413	14.656	6501
X-RAY DIFFRACTION	r_mcbond_other	4.411	14.656	6501
X-RAY DIFFRACTION	r_mcangle_it	7.592	26.361	8121
X-RAY DIFFRACTION	r_mcangle_other	7.592	26.362	8122
X-RAY DIFFRACTION	r_scbond_it	4.36	15.139	7086
X-RAY DIFFRACTION	r_scbond_other	4.346	15.132	7079
X-RAY DIFFRACTION	r_scangle_it	7.409	27.777	10200
X-RAY DIFFRACTION	r_scangle_other	7.409	27.777	10201
X-RAY DIFFRACTION	r_lrange_it	11.475	134.285	15681
X-RAY DIFFRACTION	r_lrange_other	11.475	134.284	15682
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.052	0.05	18369
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.048	0.05	18377
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.047	0.05	18439

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.05159	0.0501
1	2	A	X-RAY DIFFRACTION	Local ncs	0.05159	0.0501
2	3	A	X-RAY DIFFRACTION	Local ncs	0.04783	0.0501
2	4	A	X-RAY DIFFRACTION	Local ncs	0.04783	0.0501
3	5	A	X-RAY DIFFRACTION	Local ncs	0.04681	0.0501
3	6	A	X-RAY DIFFRACTION	Local ncs	0.04681	0.0501

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
3.95-4.052	0.375	133	0.312	2441	X-RAY DIFFRACTION	100
4.052-4.162	0.378	115	0.294	2454	X-RAY DIFFRACTION	100
4.162-4.282	0.286	130	0.265	2345	X-RAY DIFFRACTION	100
4.282-4.413	0.317	106	0.25	2334	X-RAY DIFFRACTION	100
4.413-4.556	0.265	100	0.252	2252	X-RAY DIFFRACTION	100
4.556-4.715	0.289	131	0.244	2128	X-RAY DIFFRACTION	100
4.715-4.891	0.316	130	0.245	2080	X-RAY DIFFRACTION	100
4.891-5.089	0.242	97	0.211	1986	X-RAY DIFFRACTION	100
5.089-5.312	0.208	119	0.205	1906	X-RAY DIFFRACTION	99.9506
5.312-5.568	0.246	122	0.216	1827	X-RAY DIFFRACTION	100
5.568-5.865	0.335	84	0.24	1766	X-RAY DIFFRACTION	100
5.865-6.216	0.392	81	0.243	1712	X-RAY DIFFRACTION	100
6.216-6.637	0.311	77	0.243	1562	X-RAY DIFFRACTION	100
6.637-7.158	0.219	89	0.206	1468	X-RAY DIFFRACTION	100
7.158-7.825	0.253	58	0.207	1370	X-RAY DIFFRACTION	100
7.825-8.721	0.263	67	0.216	1263	X-RAY DIFFRACTION	100
8.721-10.018	0.256	44	0.202	1121	X-RAY DIFFRACTION	99.9142
10.018-12.144	0.371	37	0.21	967	X-RAY DIFFRACTION	100
12.144-16.673	0.399	36	0.24	768	X-RAY DIFFRACTION	100
16.673-49.15	0.365	33	0.494	485	X-RAY DIFFRACTION	99.6154

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